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Dear Song,<BR>
I guess that the problem you encountered does not matter the GROMACS. On contrary, I think that you must have edited the pdb file and made mistakes of the file format so that pdb2gmx can not tell it correctly. I wish this information can help you to deal with the problem.<BR>
<BR>
xiaowu<BR>
<BR>
Yanmei Song wrote:<BR>> Dear Justin:<BR>> <BR>> Thank you so much for your help earlier. I updated my GROMACS to<BR>> 4.0.4. When I run pdb2gmx using the following two files. I still got<BR>> the similar error message:<BR>> <BR>> Opening library file ffoplsaa.rtp<BR>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat<BR>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat<BR>> WARNING: masses will be determined based on residue and atom names,<BR>> this can deviate from the real mass of the atom type<BR>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat<BR>> Entries in atommass.dat: 178<BR>> WARNING: vdwradii will be determined based on residue and atom names,<BR>> this can deviate from the real mass of the atom type<BR>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat<BR>> Entries in vdwradii.dat: 28<BR>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat<BR>> Entries in dgsolv.dat: 7<BR>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat<BR>> Entries in electroneg.dat: 71<BR>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat<BR>> Entries in elements.dat: 218<BR>> Reading pdms2.pdb...<BR>> Read 13 atoms<BR>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat<BR>> 26 out of 26 lines of xlateat.dat converted succesfully<BR>> Analyzing pdb file<BR>> There are 1 chains and 0 blocks of water and 3 residues with 13 atoms<BR>> <BR>> chain #res #atoms<BR>> 1 ' ' 3 13<BR>> <BR>> All occupancies are one<BR>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp<BR>> Atomtype 1<BR>> Reading residue database... (ffoplsaa)<BR>> Opening library file ffoplsaa.rtp<BR>> <BR>> -------------------------------------------------------<BR>> Program pdb2gmx_d, VERSION 4.0.4<BR>> Source code file: resall.c, line: 279<BR>> <BR>> Fatal error:<BR>> in .rtp file at line:<BR>> <BR>> <BR>> -------------------------------------------------------<BR>> <BR>> My new residue added to ffoplass.rtp is:<BR>> [ PDM ]<BR>> ; designation arbitrary, C1 and C2 is -CH3<BR>> [ atoms ]<BR>> SI1 SI 0.300 1<BR>> C1 opls_069 0.000 1<BR>> C2 opls_069 0.000 1<BR>> O1 opls_108 -0.300 1<BR>> <BR>> [ bonds ]<BR>> SI1 -O1<BR>> SI1 C1<BR>> SI1 C2<BR>> SI1 O1<BR>> O1 +SI1<BR>> <BR>> <BR>> ; Terminal PDMS residue ("beginning" of chain)<BR>> ; designation arbitrary, C1 C2 and C3 is -CH3<BR>> [ PDMB ]<BR>> [ atoms ]<BR>> C1 opls_069 0.000 1<BR>> SI1 SI 0.300 1<BR>> C2 opls_069 0.000 1<BR>> C3 opls_069 0.000 1<BR>> O1 opls_108 -0.300 1<BR>> <BR>> [ bonds ]<BR>> SI1 C1<BR>> SI1 C2<BR>> SI1 C3<BR>> SI1 O1<BR>> O1 +SI1<BR>> <BR>> <BR>> ; Terminal PE residue ("end" of chain)<BR>> ; designation arbitrary, C1 C2 and C3 is -CH3<BR>> <BR>> [ PDME ]<BR>> [ atoms ]<BR>> SI1 SI 0.000 1<BR>> C1 opls_069 0.000 1<BR>> C2 opls_069 0.000 1<BR>> C3 opls_069 0.000 1<BR>> <BR>> [ bonds ]<BR>> SI1 -O1<BR>> SI1 C1<BR>> SI1 C2<BR>> SI1 C3<BR>> <BR>> PDB file:<BR>> <BR>> ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00<BR>> ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00<BR>> ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00<BR>> ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00<BR>> ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00<BR>> ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00<BR>> ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00<BR>> ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00<BR>> ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00<BR>> ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00<BR>> ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00<BR>> ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00<BR>> ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00<BR>> TER<BR>> <BR>> Thanks a lot!<BR>> <BR>> <BR>> <BR>> <BR>> <BR><BR><br /><hr />使用新一代 Windows Live Messenger 轻松交流和共享！ <a href='http://www.windowslive.cn' target='_new'>立刻下载！</a></body>
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